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| Status |
Public on Oct 31, 2021 |
| Title |
M132C |
| Sample type |
SRA |
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| Source name |
Muscle
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| Organism |
Ovis aries |
| Characteristics |
sheepid: 132
Sex: female
treatment: control
tissue: Muscle
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the liver and muscle after homogenizing the tissues in Trizol reagent (Life Technologies, Carlsbad, CA) following the manufacturer’s recommendations. Any residual contaminating DNA was removed by binding the RNA in a RNeasy binding column, treating the column with RNAse free DNAse (Qiagen, Germantown, MD) and eluting the RNA in nuclease free water. The quality of purified RNA including the purity and RNA integrity were evaluated using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) at the University of Michigan Advanced Genomics Core.
library preparation was carried out using TruSeq RNA Library Prep Kit (Illumina, San Diego, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
39271_GCCAAT
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| Data processing |
Raw fastq files from total RNA sequencing data were trimmed using trimmomatic
Trimmed reads from total RNA were further mapped to sheep reference genome (Oar_rambouillet_v1.0) using Spliced Transcripts Alignment to a Reference (STAR) aligner (2.6.0c)
The reads that aligned to the exons of the reference genome were then counted using featureCounts (1.6.1)
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: matrix table of normalized gene counts for each sample
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| Submission date |
Jun 23, 2021 |
| Last update date |
Oct 31, 2021 |
| Contact name |
Kelly Bakulski |
| E-mail(s) |
bakulski@umich.edu
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| Organization name |
University of Michigan
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| Department |
Department of Epidemiology
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| Street address |
1415 Washington Heights
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL15670 |
| Series (2) |
| GSE178774 |
Developmental Programming: Impact of prenatal testosterone excess on liver and muscle transcriptome and the relationship between non-coding and coding RNA networks in female sheep [RNA-seq] |
| GSE178777 |
Developmental Programming: Impact of prenatal testosterone excess on liver and muscle transcriptome and the relationship between non-coding and coding RNA networks in female sheep |
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| Relations |
| BioSample |
SAMN19838942 |
| SRA |
SRX11208051 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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